rs1186919

chr5-157893268-G-Achr5-157893268-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.806 in 152,172 control chromosomes in the GnomAD database, including 50,084 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (50084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122539 AN: 152054 Hom.: 50062 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.789

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.806 AC: 122614 AN: 152172 Hom.: 50084 Cov.: 32 AF XY: 0.805 AC XY: 59907 AN XY: 74402

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.785

Alfa AF: 0.804 Hom.: 102123

Bravo AF: 0.788

Asia WGS AF: 0.602 AC: 2098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.019
Dann	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1186919; hg19: chr5-157320276;